19-4543904-C-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_032108.4(SEMA6B):c.2364G>C(p.Pro788Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000474 in 1,202,224 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00027 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000016 ( 0 hom. )
Consequence
SEMA6B
NM_032108.4 synonymous
NM_032108.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.555
Genes affected
SEMA6B (HGNC:10739): (semaphorin 6B) This gene encodes a member of the semaphorin family, a group of proteins characterized by the presence of a conserved semaphorin (sema) domain. Whereas some semaphorins are transmembrane proteins, others are secreted. Semaphorins play a major role in axon guidance. The protein encoded by this gene may be involved in both peripheral and central nervous system development. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
Variant 19-4543904-C-G is Benign according to our data. Variant chr19-4543904-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 792322.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.555 with no splicing effect.
BS2
High AC in GnomAd4 at 40 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000266 AC: 40AN: 150210Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
40
AN:
150210
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
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GnomAD4 exome AF: 0.0000162 AC: 17AN: 1051910Hom.: 0 Cov.: 33 AF XY: 0.0000201 AC XY: 10AN XY: 496362 show subpopulations
GnomAD4 exome
AF:
AC:
17
AN:
1051910
Hom.:
Cov.:
33
AF XY:
AC XY:
10
AN XY:
496362
Gnomad4 AFR exome
AF:
AC:
15
AN:
21698
Gnomad4 AMR exome
AF:
AC:
1
AN:
7442
Gnomad4 ASJ exome
AF:
AC:
0
AN:
12762
Gnomad4 EAS exome
AF:
AC:
0
AN:
23744
Gnomad4 SAS exome
AF:
AC:
0
AN:
19288
Gnomad4 FIN exome
AF:
AC:
0
AN:
20620
Gnomad4 NFE exome
AF:
AC:
0
AN:
902196
Gnomad4 Remaining exome
AF:
AC:
1
AN:
41444
Heterozygous variant carriers
0
1
3
4
6
7
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
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>80
Age
GnomAD4 genome AF: 0.000266 AC: 40AN: 150314Hom.: 0 Cov.: 32 AF XY: 0.000286 AC XY: 21AN XY: 73422 show subpopulations
GnomAD4 genome
AF:
AC:
40
AN:
150314
Hom.:
Cov.:
32
AF XY:
AC XY:
21
AN XY:
73422
Gnomad4 AFR
AF:
AC:
0.000925114
AN:
0.000925114
Gnomad4 AMR
AF:
AC:
0.000132626
AN:
0.000132626
Gnomad4 ASJ
AF:
AC:
0
AN:
0
Gnomad4 EAS
AF:
AC:
0
AN:
0
Gnomad4 SAS
AF:
AC:
0
AN:
0
Gnomad4 FIN
AF:
AC:
0
AN:
0
Gnomad4 NFE
AF:
AC:
0
AN:
0
Gnomad4 OTH
AF:
AC:
0
AN:
0
Heterozygous variant carriers
0
3
6
8
11
14
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Variant carriers
0
2
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6
8
10
<30
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>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Dec 31, 2019
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at